In these two zip files all OMA output files are included. 

"OMA_Crustacea_all_OrthologousGroupsFasta" includes the OMA output used for the analyses of the all taxon matrices (1-5) as well as the Malacostracan specific matrix. For the latter, all non-Malacostracans were removed from these files.

A few taxa were removed after OMA finished and were not included in the respective analyses (either to avoid duplicates [e.g. Remipedia] or to exclude low coverage species):

Crust175	SAMN06174150
Crust172d	SAMN06174147
Crust150	SAMN06174135
Crust151	SAMN06174136
Crust136	SAMN06174130
Crust130B	SAMN05717820
Crust128	SAMN05717822
Crust117	SAMN06174125
SRR1233153
Crust102     (this is Eoleptestheria; the first Trinity assembly of Eoleptestheria contained some errors and was tehrefore removed formt this run; a corrected assembly was included only in the Branchiopod specific atrix due to computational limitations)




"OrthologousGroupsFasta_Branchiopoda" includes the OMA output for the Branchiopod specific matrix. OMA was newly computed or the Branchiopoda to include Eoleptestheria ticinensis.




List of species names, GenBank accession numbers and internal numbers:

Species	GenBank accession 	internal_number
Ixodes scapularis	ensembl.org	
Strigamia maritima	ensembl.org	
Euphausia crystallorophias	ERR264582 	
Anoplodactylus eroticus	SAMN04910999	
Branchinella herrodi	SAMN05717805	Crust105
Triops australiensis	SAMN05717806	Crust142
Ozestheria rubra	SAMN05717807	Cae640
Hutchinsoniella macracantha	SAMN05717808	Crust178
Lightiella incisa	SAMN05717809	Crust200
Calanus finmarchicus	SAMN05717810	Crust123
Temora longicornis	SAMN05717811	Crust125
Speonebalia cannoni	SAMN05717812	Crust138
Palaemon suttkusi	SAMN05717813	Crust115B
Neogonodactylus bredini	SAMN05717814	Crust170a
Caprella sp.	SAMN05717815	Crust160
Cylindroleberidinae	SAMN05717816	Crust197
Paranesidea sp.	SAMN05717817	Crust198
Eusarsiella sp.	SAMN05717818	Crust176b
Lasionectes entrichoma	SAMN05717819	Crust139
Xibalbanus tulumensis	SAMN05717821	Crust116
Chthamalus fragilis	SAMN05717823	Crust169a
Derocheilocaris remanei	SAMN05717824	Crust194
Procambarus clarkii	SAMN06169695	PC_HPT
Eulimnadia sp.	SAMN06174118	Crust101
Eoleptestheria cf. ticinensis	SAMN06174119	Crust102
Limnadopsis birchii	SAMN06174120	Crust103
Limnadopsis parvispinus	SAMN06174121	Crust104
Simocephalus vetulus	SAMN06174122	Crust107
Ceriodaphnia cf. quadrangula	SAMN06174123	Crust108
Sida crystallina	SAMN06174124	Crust110
Ozestheria sp. K 	SAMN06174126	Cae645
Polyphemus pediculus	SAMN06174127	Crust126
Anchistropus emarginatus	SAMN06174128	Crust127
Typhlatya sp.	SAMN06174129	Crust129
Cyclestheria hislopi	SAMN06174131	Crust145
Cyclestheria hislopi	SAMN06174132	Crust146
Eocyzicus sp. W	SAMN06174133	Crust147
Eurycercus cf. lamellatus	SAMN06174134	Crust148
Podon leuckartii	SAMN06174137	Crust155b (LB2)
Evadne cf. nordmanni	SAMN06174138	Crust156d (LB8)
Pagurus longicarpus	SAMN06174139	Crust157
Semibalanus balanoides	SAMN06174140	Crust159
Praunus flexuosus	SAMN06174141	Crust161a2
Crangon septemspinosa	SAMN06174142	Crust162a
Bosmina sp. 	SAMN06174143	Crust165a
Scapholeberis cf. mucronata	SAMN06174144	Crust166b
Farfantepenaeus duorarum	SAMN06174145	Crust171a
Loxothylacus texanus	SAMN06174146	Crust172b
Emerita talpoida	SAMN06174148	Crust173a
Homarus americanus	SAMN06174149	Crust174
Idotea baltica	SAMN06174151	Crust181
Libinia emarginata	SAMN06174152	Crust182
Stenopus hispidus	SAMN06174153	Crust183a
Enoplometopus cf. daumi	SAMN06174154	Crust184a
Thamnocephalus platyurus	SAMN06174155	Crust185a
Streptocephalus sp.	SAMN06174156	Crust186a
Branchinecta lindahli	SAMN06174157	Crust187a
Eulimnadia texana	SAMN06174158	Crust188a
Moina sp.	SAMN06174159	Crust190a
Pollicipes  polymerus	SAMN06174160	Crust191a
Neotrypaea californiensis	SAMN06174161	Crust192a
Leptochelia sp.	SAMN06174162	Crust195
Rutiderma sp.	SAMN06174163	Crust196
Panulirus argus	SAMN06174164	Crust199
Anaspides tasmaniae	SAMN06174165	Crust201B
Cumella sp.	SAMN06174166	Crust203
Triops longicaudatus	SAMN06174167	Crust204
Triops granarius	SAMN06174168	Crust205
Conchoecia obtusata	SAMN06174169	Crust207
Artemia salina	SAMN06174170	Crust208
Macrotrichidae	SAMN06174171	Crust209a
Lepidurus cryptus	SAMN06174172	Crust211
Lynceus sp.	SAMN06174173	Crust214
Cyzicus pilosus	SAMN06174174	Crust215
Paralimnadia urukhai	SAMN06174175	Crust219
Metalimnadia sp.	SAMN06174176	Crust223
Eucyclops serrulatus	SRR1050725	
Echinogammarus veneris	SRR1050726	
Eurytemora affinis	SRR1104127	
Lernaea cyprinacea	SRR1107498	
Limulus polyphemus	SRR1145732	
Leucauge venusta	SRR1145740	
Cryptops hortensis	SRR1153457	
Craterostigmus tasmanianus	SRR1157986	
Metabetaeus lohena	SRR1248247, SRR1248249	
Tigriopus californicus	SRR1626906	
Cherax destructor	SRR1813039	
Penaeus vannamei	SRR346404, SRR1951373, SRR1407791	
Argulus siamensis	SRR514120	
Acerentomon sp. AD-2013	SRR921562	
Anurida maritima	SRR921564	
Meinertellus cundinamarcensis	SRR921617	
Occasjapyx japonicus	SRR921624	
Thermobia domestica	SRR921648	
Glomeridesmus sp.	SRR941771	
Drosophila melanogaster	translated peptides from flybase.org	
Daphnia pulex	wfleabase	
 